Author: Chris

  • How to design a digest to screen minipreps after a ligation.

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    Chris
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    MacVector’s Agarose Gel tool can be used to quickly design a restriction digest to screen minipreps following a ligation.  Replicate your ligation in MacVector. Select the two sites, for subcloning your targeted gene, and click DIGEST. Drag the digested fragment from the Cloning Clipboard to your vector click LIGATE. Create your agarose gel with the…

  • MacVectorTip: Grayed out graphics indicate Missing Features

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    Chris
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    If the graphics in a nucleic acid sequence Map tab appear somewhat “washed out” it is because the graphic items represent common features that MacVector has found that are not annotated on the sequence. For example, here are the Map and Feature tabs of an unannotated cloning vector; You can see a number of features…

  • MacVectorTip: “Nudge” Reads for Better Reference Alignments

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    Chris
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    The MacVector alignment algorithms are usually pretty good at finding the optimum alignments of reads against a reference sequence. But, very occasionally, they may get confused by repeats or other anomalies in the sequences. Or perhaps you have made after-the-alignment edits: for example, in the Align to Reference Editor, you can insert residues by holding…

  • MacVectorTip: Trimming by Quality in sequence assemblies

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    Chris
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    Many of our users may be familiar with the ability of Sequencher to semi-automatically trim poor quality sequences from the ends of Sanger ABI reads. Although it is generally not necessary to do this in MacVector because most of the algorithms can automatically handle poor quality data, there are times when it can be beneficial.…

  • MacVectorTip: Use self comparison matrix analysis to identify repeats and inversions

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    Chris
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    The Dot-Plot analysis (Pustell DNA Matrix) function in MacVector is an extremely powerful way of quickly getting an overview of the similarities between a pair of sequences. However, it can also be used to identify repeats and inversions in a single DNA sequence simply by comparing a sequence to itself. For example here is the…

  • MacVectorTip: Restriction enzyme sites and tooltips

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    Chris
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    Quickly viewing the recognition sequence and cut site of a restriction site is very easy in the Map tab. By default MacVector’s Scan DNA For… tool will automatically display restriction enzyme recognition sites in the Map tab. If you hover your mouse over a restriction site, a tooltip will show you the restriction enzyme recognition site, the location of the cut…

  • MacVectorTip: Advanced Align to Reference Editing

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    Chris
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    You can use the Analyze | Align to Reference function to align other sequences (Sanger chromatograms, plain sequences or even NGS data collections) against a reference. Once aligned, the Editor lets you perform all the usual editing functions using an “overwrite” mode – select the residue you want and type the new residue to replace…

  • MacVectorTip: How to Toggle Between Single-Letter and Three-Letter Amino Acid Translation Code

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    Chris
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    Many views in MacVector display amino acid translations above or below DNA sequences. Typically, these are from CDS features, but can also be the 3/6 frame translation of a sequence. You can display the amino acids as either the single-letter code, or as the three-letter code. You can toggle the setting using the MacVector | Preferences ->…

  • MacVectorTip: Drag and drop in the Gibson Assembly window

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    Chris
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    Over the years, we have added a lot of drag and drop functionality to MacVector. Of course, as with any application, it is not always obvious that you can drag and drop to accomplish tasks because you literally have to drag and drop to discover you can do it at all! So here is the first of…

  • MacVectorTip: organizing assemblies and sequencing datasets with the Assembly Project manager.

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    Chris
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    MacVector’s Assembly Project manager helps you organize multiple sequencing datasets, multiple reference sequences and repeated assemblies. You can store multiple assembly jobs in a single Assembly Project and directly compare multiple runs of the same dataset to determine the best assembly parameters. You can also compare different sequencing datasets assembled against the same reference sequence…